I do not know which version of RoundCube is within the package.
I use RoundCube for quiet some time now as a second webmail client for my clients, because it is still in Beta.
I've setup RoundCube according my own howto, which you can find here:http://www.howtoforge.com/roundcube_webmail_ispconfig, using the latest Roundcube version.
Soon i will change the howto, so that it is also possible to login with [email protected].
With my setup and at the moment it is only possible to login with the lohin name as defined within ISPConfig.

Personally, I prefer this method, because i can maintain it myself with full control over the version and at it will work on port 80.

I would install RoundCube from scratch again in the webspace of your choice.
If you want, you can export your old RoundCube database and import it into the new one, but i think it's only necesarry for extra functions like the addressbook.

The webmailclient is only a way to read the content of your mailboxes.
If the boxes Inbox, Sentbox, Spambox, Trashbox, are the default ones in the RoundCube package version, i do not expect problems, because i use these boxes too. In other words, your users can see there mail again, if you make a new setup.

If you've phpmyadmin installed, you can easily find it, when you login with your mysql root account.
You can download the phpmyadmin package for ISPConfig at the documentation section at http://www.ispconfig.org.
Install it with the update manager within ISPConfig.